anndata
anndata: Access and store annotated data matrices - Published in JOSS (2024)
starfish
starfish: scalable pipelines for image-based transcriptomics - Published in JOSS (2021)
unitvelo
UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference
GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
https://github.com/alleninstitute/scrattch
Single cell RNA-seq analysis for transcriptomic type characterization
DIscBIO
A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics
macrophage-regulation
Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation
bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
molkart
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
https://github.com/alleninstitute/scrattch.hicat
Hierarchical, iterative clustering for analysis of transcriptomics data in R
https://github.com/alleninstitute/tasic2016data
Single cell transcriptomic data from Tasic, et al. (2016)
iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
EWCE
Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
cluefish
A specialised workflow designed to enhance the biological interpretation of transcriptomic data series 🎣
rnalysis
Analyze your RNA sequencing data without writing a single line of code
fishpond
Differential expression and allelic analysis, nonparametric statistics
scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
pyscenic
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
curare
Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments
digitalcellsorter
Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:
https://github.com/cran-task-views/omics
CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics
https://github.com/alleninstitute/scrattch.vis
scRNA-seq data visualization from scrattch
https://github.com/biomedsciai/biomed-multi-omic
Build foundation model on RNA or DNA data
https://github.com/becavin-lab/bacnet
BACNET is a Java based platform to develop website for multi-omics analysis
volcano3d
An R package to plot interactive three-way differential expression analysis
icetea
R/Bioconductor package for analysis of single and paired-end capped-RNAseq data (CAGE/RAMPAGE/MAPCap)
imsig
Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
https://github.com/a-r-j/tb-resources
List of online databases and resources for Mycobacterium Tuberculosis
https://github.com/bayer-group/cellenium
Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).
https://github.com/alleninstitute/scrattch.io
Functions for handling RNA-seq files and formats as input and output for scrattch functions.
https://github.com/bgeedb/bgee_pipeline
Source code of the Bgee pipeline used to build the Bgee database
singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
isocomp
Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq
tfactivity
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
https://github.com/broadinstitute/temporal-rna-seq-deconvolution
Package for temporal deconvolution of bulk RNA-seq samples using SVI
tucca-rna-seq
Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects
zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
https://github.com/daisybio/DysRegNet_package
Inferring patient-specific regulatory alterations
https://github.com/alleninstitute/lowcat
Low coverage accessibility and transcriptomics
bd-lithium
A collection of source codes for network-based multi-omics analysis using integrated genome-wide association studies (GWAS) and transcriptomic data to identify genetic contribution into lithium response in patients with bipolar disorder (BD).
rich_directrna
Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives